The web archive is indeed changed by editing as expected but not by DEVONthink on its own. When updating a web archive, the URL property is then automatically set to the internal URL of the web archive (due to former requests to ensure consistency of these two URLs).
But in this case without a URL and an invalid file URL this doesn’t make sense, the next release will fix this.
BTW:
For long term storage, web archives are actually not recommended as they’re limited to Apple’s platforms. In addition, web archives created on current macOS versions are not always compatible to older macOS versions.